Freesurfer November 2016

freesurfer@nmr.mgh.harvard.edu

120 participants
214 discussions

Recon reprocessing control points error
by Sarah Finnegan 09 Nov '16

09 Nov '16

Hi there, I am using freesurfer v5.3.0 to recon some 7T structural scans. I have been adding some control points to compensate for poor temporal lobe contrast, something that has worked just fine many times before. However, now when rerunning the recon process as follows: recon-all -autorecon2-cp -autorecon3 -subjid <name> It looks like the reprocessing has not taken the control points into account at all, and actually has changed the segmentation in areas that were previously fine. My control.dat file is in the subjid/tmp folder and is populated correctly so I assume it should be able to be located. Can anyone offer any advice on what might be going on? The same error is also being experienced by a colleague here. Thanks a lot! Sarah Finnegan Nuffield Department of Clinical Neurosciences University of Oxford, John Radcliffe Hospital Oxford, OX3 9DU Email: sarah.finnegan(a)stcatz.ox.ac.uk<mailto:sarah.finnegan@stcatz.ox.ac.uk>

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Longitudinal Stream on HCP Data
by Timothy Hendrickson 08 Nov '16

08 Nov '16

Aww thank you for clarifying Michael. I definitely misread Matthew's post. -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay)

1 0

Fwd: [HCP-Users] HCP to FreeSurfer Resampling
by Timothy Hendrickson 08 Nov '16

08 Nov '16

FreeSurfer experts, I am attempting to resample HCP data into FreeSurfer space with the following how to document: https://wiki.humanconnectome. org/display/PublicData/HCP+Users+FAQ. <https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ> I believe I have resampled the GIFTI file into fs_average space, however I am running to problems visualizing it in freeview or tksurfer. Please see the error message in the forwarded message below? -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) ---------- Forwarded message ---------- From: Timothy Hendrickson <hendr522(a)umn.edu> Date: Tue, Nov 8, 2016 at 8:51 AM Subject: Re: [HCP-Users] HCP to FreeSurfer Resampling To: Timothy Coalson <tsc5yc(a)mst.edu> Cc: "hcp-users(a)humanconnectome.org" <HCP-Users(a)humanconnectome.org> Hi Tim, Thank you for taking a look at my script, I really appreciate it. I am now running into another problem. After re-sampling into fs_average space I am attempting to visualize that file as an overlay in tksurfer or freeview (freesurfer visualization tools) however I receive the following error: *mriseadGIFTIfile: mris is NULL! found when parsing file rh.43242.32k_TJH_fsavg.func.gii*. I know that freesurfer can handle GIFTI file so that is not the problem. I wonder if the GIFTI file was created incorrectly... Any advice? -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay)

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Re: [Freesurfer] mapping ROI to surface space
by Bruce Fischl 08 Nov '16

08 Nov '16

Hi Derek I'll cc the FS list so others can answer. It depends on the reason the holes exist. It also depends on the size of the holes. The dev version of mri_label2labels supports morphological close operations. It takes an integer parameter which should be about the radius of the holes you would like to fill in. Note that this will also fill in some concavities in the boundary of the label. cheers Bruce On Tue, 8 Nov 2016, Andrews, Derek wrote: > Hi Bruce, > > Apologies for contacting you directly but I’m not sure if my message is > getting through to the list. > > I have gotten ahold of the dev version of mri_label2label. > > Currently I have a .w file that I need to “fill in the holes” on. Could > you please specify the steps I will need to take to make my .w file an > acceptable input for mri_label2label, and any recommendations you may have > for the value of N for the —close flag. > > Any help you could provide would be appreciated. > > Best, Derek > > > > > ________________________________________ > Derek Sayre Andrews, MSc > PhD Candidate > > The Sackler Institute for Translational Neurodevelopment > Department of Forensic and Neurodevelopmental Sciences > Institute of Psychiatry, Psychology & Neuroscience, King's College London > > Telephone: +44 (0)20 7848 5701 > Email: Derek.Andrews(a)kcl.ac.uk > > > > > > On 28/10/2016 15:53, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: > >> Hi Derek >> >> I think the dev version of mri_label2label supports >> open/close/dilate/erode >> operations: >> >> mri_label2label --help >> USAGE: mri_label2label.bin >> >> --srclabel input label file >> >> --erode N erode the label N times before writing >> --open N open the label N times before writing >> --close N close the label N times before writing >> --dilate N dilate the label N times before writing >> . >> . >> . >> >> if your version doesn't have these operations let us know and we can get >> you an updated one >> >> cheers >> Bruce >> >> >> >> On Fri, 28 Oct 2016, >> Andrews, Derek wrote: >> >>> Hi Bruce, >>> >>> As always thank you for your prompt reply. >>> >>> For the morphological close operation, would you suggest using mris_fill >>> on the surface ROI I created and then running mri_vol2surf again on the >>> volume output by mris_fill? >>> >>> Best, Derek >>> >>> >>> ________________________________________ >>> Derek Sayre Andrews, MSc >>> PhD Candidate >>> >>> The Sackler Institute for Translational Neurodevelopment >>> Department of Forensic and Neurodevelopmental Sciences >>> Institute of Psychiatry, Psychology & Neuroscience, King's College >>> London >>> >>> Telephone: +44 (0)20 7848 5701 >>> Email: Derek.Andrews(a)kcl.ac.uk >>> >>> >>> >>> >>> >>> On 28/10/2016 14:54, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: >>> >>>> p.s. you could remove many/most of these holes using a morphological >>>> close operation >>>> On Fri, 28 Oct 2016, Andrews, Derek wrote: >>>> >>>>> Hello Freesurfer Developers and Community, >>>>> >>>>> I am looking to map a ROI.nii based on the MNI152 template to the >>>>> fsaverage >>>>> pial surface. >>>>> >>>>> I have used the following commands >>>>> >>>>> Bbregister ‹s fsaverage ‹mov MNI152.nii ‹reg register.dat ‹init-fsl >>>>> ‹12 >>>>> ‹t1 >>>>> >>>>> Then >>>>> >>>>> mri_vol2surf ‹src ROI.nii ‹out ROI.mgh ‹srcreg register.dat ‹hemi lh >>>>> >>>>> The ROI appears to be in the right place however is very blotchy. >>>>> Have I >>>>> missed a step? Or is this correct? >>>>> >>>>> See bellow a picture of the ROI highlighted in FSL and in tksurfer >>>>> after >>>>> mapped using the above. >>>>> >>>>> Thank you for your support, >>>>> >>>>> Best, Derek >>>>> >>>>> [IMAGE] >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________________________________ >>>>> __ >>>>> ___ >>>>> >>>>> Derek Sayre Andrews, MSc >>>>> PhD Candidate >>>>> >>>>> The Sackler Institute for Translational Neurodevelopment >>>>> >>>>> Department of Forensic and Neurodevelopmental Sciences >>>>> >>>>> Institute of Psychiatry, Psychology & Neuroscience, King's College >>>>> London >>>>> >>>>> Telephone: +44 (0)20 7848 5701 >>>>> Email: Derek.Andrews(a)kcl.ac.uk >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> >>>> https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail. >>>> nm >>>> >>>> r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cderek >>>> .a >>>> >>>> ndrews%40kcl.ac.uk%7C65ef7af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c16 >>>> b8 >>>> >>>> 3c724071654356%7C0&sdata=liaieNpnjB7M4w9favIeZ9B0ZrooUbfDThLvJxmbcuo%3D& >>>> re >>>> served=0 >>>> >>>> >>>> The information in this e-mail is intended only for the person to whom >>>> it >>>> is >>>> addressed. If you believe this e-mail was sent to you in error and the >>>> e-mail >>>> contains patient information, please contact the Partners Compliance >>>> HelpLine at >>>> >>>> https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.pa >>>> rt >>>> >>>> ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C65e >>>> f7 >>>> >>>> af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c16b83c724071654356%7C0&sdata >>>> =% >>>> 2F%2Fl3dvHGeXDJCkpHGWdvv9sI59QW76kFK%2FK1HdUQZnE%3D&reserved=0 . If the >>>> e-mail was sent to you in error >>>> but does not contain patient information, please contact the sender and >>>> properly >>>> dispose of the e-mail. >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> >>> https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.n >>> mr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cderek >>> .andrews%40kcl.ac.uk%7C619839454aa24e2abb5b08d3ff423c1d%7C8370cf1416f34c1 >>> 6b83c724071654356%7C0&sdata=b7RxteOygtLeOXwEqb7jklBy8UF4yYIW2P08all9jKQ%3 >>> D&reserved=0 >>> >>> >>> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nm >> r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cderek.a >> ndrews%40kcl.ac.uk%7C619839454aa24e2abb5b08d3ff423c1d%7C8370cf1416f34c16b8 >> 3c724071654356%7C0&sdata=b7RxteOygtLeOXwEqb7jklBy8UF4yYIW2P08all9jKQ%3D&re >> served=0 >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.part >> ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C61983 >> 9454aa24e2abb5b08d3ff423c1d%7C8370cf1416f34c16b83c724071654356%7C0&sdata=y >> glzZIazWf12gfszA3LPiOPVUl9m2jppoYC8oUjsrlI%3D&reserved=0 . If the e-mail >> was sent to you in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. > > > >

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Longitudinal Stream on HCP Data
by Timothy Hendrickson 08 Nov '16

08 Nov '16

Hi Freesurfer/HCP experts, I am curious if there is a way to incorporate HCP data (i.e. myelin maps) into the FreeSurfer processing stream. Matthew Glasser mentioned in a post on the HCP mailing list about a month back that this is being actively worked on by FreeSurfer: http://www.mail-archive.com/hcp-users@humanconnectome.org/msg03477.html. <http://www.mail-archive.com/hcp-users@humanconnectome.org/msg03477.html> Are there any workflows or development versions that I can download in order to perform something like this. Respectfully, -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay)

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recon-all steps question
by miracle ozzoude 08 Nov '16

08 Nov '16

Hello Freesurfer, I have couple of questions. While going through the frequently asked questions on your page http://freesurfer.net/fswiki/UserContributions/FAQ I came across a question regarding how to integrate a skull stripped from another problem into freesurfer (using recon-all -autorecon1 -noskullstrip -s subjid ----> create a symbolic link from T1.mgz to brainmask.auto.mgz and another like from brainmask.auto.mgz to brainmask.mgz ------> after run the finall stages of recon-all: recon-all -autorecon2 -autorecon3 -s subjid). First question, isn't T1.mgz, brainmask.auto.mgz and brainmask.mgz created during skull stripping? why are they present if I included the "-no skullstrip" flag? Second question, where do I insert my already skull stripped data in the symbolic link? Last question, the final stages of recon-all doesn't include skull stripping, how can I be sure my skull stripped data was incorporated into the freesurfer recon-all process? Best, Paul

3 15

perl & bbregister conflicts
by GREGORY R KIRK 08 Nov '16

08 Nov '16

Hi folks, somebody stuck me with Ubuntu 16 for a month and I found the perl problem and so switched to the dev version which solved that problem. discovered that with the dev version bbregister throws an error having to do with fsl flirt throws an error `terminate after throwing an instance of NEWMAT::SingularException the version of fsl i have installed is 5.0 of course so i use dev for recon and 5.3 for bbregister so just to let you know the bbregister/fsl problem is there in the latest dev cheers Greg

3 2

Qdec plot design
by Mihaela Stefan 07 Nov '16

07 Nov '16

Hello Freesurfers, I am doing a group analysis using Qdec. I have a few significant clusters and I would like to plot one of them. Qdec does that if I click on 'Find Clusters and Goto Max' but I don't see options for the design of the plot. How can I export the thickness values from my cluster to reproduce the Qdec plot in another program? Thank you! Mihaela

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MRI Freesurfer
by Daniel Alejandro Reyna Torres 07 Nov '16

07 Nov '16

Hello, my name is Daniel Reyna, I am currently working with Freesurfer to analyse the cortical segmentations and parecellations that the program outputs. I have analysed some MRI but I am not sure whether I have achieve best results or probably there is something I should improve. One question is the input type. I have used dicom files but, the type of MRI should it be an axial or sagital view, or any? It seemes that Freesurfer accepts either type of MRIs, I just wanna be sure that the program is contioned for those type of MRIs. Second, is there any special recommendation for the quality or characteristics of the MRI?, i.e., the number of layers per each 3D MRI, resolution, size of voxel ... I ask this so I can ask the labs for specific conditions to maximise results with the reconstruction in Freesurfer. I currently receive images from several labs, they have different protocols for making the brain scan. I´ve been told that I could ask them for "special conditions" if that is the case. Thank you very much! Best regards, Daniel Reyna

2 1

Cortical white matter
by Del Re, Elisabetta 07 Nov '16

07 Nov '16

Dear FreeSurfer team, does the cortical white matter volume include the cerebellum? Thank you, regards, Elisabetta

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Freesurfer November 2016